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doi:10.1016/j.compbiolchem.2005.08.003    
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Copyright © 2005 Elsevier Ltd All rights reserved.

A family of metrics for biopolymers based on counting independent sets

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J. RochaCorresponding Author Contact Information, E-mail The Corresponding Author, M. LlabrésE-mail The Corresponding Author and R. AlberichE-mail The Corresponding Author

Department of Mathematics and Computer Science, Research Institute of Health Science (IUNICS), University of the Balearic Islands, 07122 Palma de Mallorca, Spain


Received 12 May 2005; 
revised 9 August 2005; 
accepted 9 August 2005. 
Available online 10 October 2005.

Abstract

We introduce a new family of metrics for graphs of fixed size, based on counting-independent sets. Our definition is simpler and easier to calculate than the edge ideal metric family defined by Llabrés and Rosselló without loosing any of its abstract properties. We contrast them on some examples with graphs that represent protein secondary and three-dimensional (3D) structures. We conclude that although the edge ideal metrics are faster to calculate on some sparse graphs, in general, the independent set metrics are more tractable.

Keywords: Counting-independent sets; Graph distance; Edge ideal metric; Hilbert polynomial; Cliques

Article Outline

1. Introduction
2. Metric definitions
3. Relationship with edge ideal metrics
4. Examples
4.1. Protein secondary structures
4.2. Protein 3D structures
4.3. More examples
5. Conclusion
Acknowledgements
References





Corresponding Author Contact InformationCorresponding author. Tel.: +34 971172969; fax: +34 971173003.

 
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